After digesting what information we do have about the whole Roger McDowell incident, I've boiled my opinion down to one question, as simplistic as that may be. If this same act had been committed by the team's star player, should that player be let go?
It seems easy to fire a coach or a manager, but if we choose to hold everyone to the same standard, and I think we should, we have to apply this same litmus test to any person on the team; be they a player or a coach.
Roger may have crossed some lines and he certainly embarrassed the team, but while he did threaten fans he did not act on those threats, so all we're left with are hurtful words. The standard in sports seems to be to give people a second chance in situations like this. Had he entered the stands or thrown something into the stands the situation would be different, as too should the penalty.
In the case of violence against fans, dismissal is the harshest punishment a team or league can enact, and it should be reserved for those extreme cases. A situation like this where only the threat of violence was involved should result in less severe punishment.
A multi-game suspension, and a hefty fine should be Roger's punishment ... and that action should come from the Atlanta Braves. The team should not wait for the commissioner to take action. If they are fully aware of the facts, which I have to assume they are by now, then the team should be the one to censure their own.